Transcriptome Analysis Reveals the Effect of Long Intergenic Noncoding RNAs on Pig Muscle Growth and Fat Deposition

Abstract

Muscle growth and fat deposition are the two important biological processes in the development of pigs which are closely related to the pig production performance. Long intergenic noncoding RNAs (lincRNAs), with lack of coding potential and the length of at least 200nt, have been extensively studied to play important roles in many biological processes. However, the importance and molecular regulation mechanism of lincRNAs in the process of muscle growth and fat deposition in pigs are still to be further studied comprehensively. In our study, we used the data, including liver, abdominal fat, and longissimus dorsi muscle of 240 days' age of two F2 full-sib female individuals from the white Duroc and Erhualian crossbreed, to identify 581 putative lincRNAs associated with pig muscle growth and fat deposition. The 581 putative lincRNAs shared many common features with other mammalian lincRNAs, such as fewer exons, lower expression levels, and shorter transcript lengths. Cross-tissue comparisons showed that many transcripts were tissue-specific and were involved in the important biological processes in their corresponding tissues. Gene ontology and pathway analysis revealed that many potential target genes (PTGs) of putative lincRNAs were involved in pig muscle growth and fat deposition-related processes, including muscle cell proliferation, lipid metabolism, and fatty acid degradation. In Quantitative Trait Locus (QTLs) analysis, some PTGs were screened from putative lincRNAs, MRPL12 is associated with muscle growth, GCGR and SLC25A10 were associated with fat deposition, and PPP3CA, DPYD, and FGGY were related not only to muscle growth but also to fat deposition. Therefore, it implied that these lincRNAs might participate in the biological processes related to muscle growth or fat deposition through homeostatic regulation of PTGs, but the detailed molecular regulatory mechanisms still needed to be further explored. This study lays the molecular foundation for the in-depth study of the role of lincRNAs in the pig muscle growth and fat deposition and further provides the new molecular markers for understanding the complex biological mechanisms of pig muscle growth and fat deposition.

Figure 1

(a) Integrative pipeline for the identification of putative lincRNAs in this study. (b) Venn diagram of all lincRNAs and novel lincRNAs and differentially lincRNAs. (c) The chromosome distribution of putative lincRNAs.

Figure 2

Characteristics of putative lincRNAs (compare with protein-coding gene). (a) Comparison of transcript length distribution. (b) Comparison of exon length distribution. (c) Comparison of exon number.

Figure 3

Expression profile of lincRNAs. (a) Comparison of expression level between lincRNAs (known and novel) and protein-coding genes. The curve indicates density distribution. (b) Differential lincRNAs expression heat map in abdominal fat vs. longissimus dorsi muscle group. (c) Differential lincRNAs expression heat map in abdominal fat vs. liver group. (d) Differential lincRNAs expression heat map in longissimus dorsi muscle vs. liver group. (e) Expression heat map of differentially expressed protein-coding genes in all tissues.

Figure 4

(a) Gene ontology and pathway analysis related to muscle growth and fat deposition of the potential target genes (PTGs) of differentially expressed lincRNAs (DELs). (b) Among the gene ontology and pathway analysis that are enriched, there are several major links between pathways involved in muscle growth and fat deposition. The blue module represents kegg pathway analysis and the green module represents gene ontology. The target gene between the two modules represents that this target gene coexists in the two pathways. For example, CPT1A exists in both glucagon signaling pathway and fatty acid degradation pathway, and most of these target genes are related to muscle growth or fat deposition.

Figure 5

(a) Venn diagram of QTLs associated with growth and fat deposition and all QTLs. (b) Distribution of lincRNAs involved in QTLs associated with growth and fat deposition on chromosomes. (c) The target genes within the range of 100kb for lincRNAs corresponding to QTLs related to muscle growth and fat deposition; the figure shows the relationship between these target genes and lincRNAs. (d) The target genes within the range of 10kb for lincRNAs corresponding to QTLs related to muscle growth and fat deposition; the figure shows the relationship between these target genes and lincRNAs and the relationship between these target genes and muscle growth or fat deposition.

Figure 6

(a-d) The target genes within the range of 10kb for lincRNAs corresponding to QTLs related to muscle growth and fat deposition, and the interaction of these major target genes with the biological processes of muscle growth or fat deposition in related pathways.

Figure 7

Linear regression of lincRNAs and its PTGs expression. The r₀ and p₀ indicate the Pearson correlation coefficient and p-value of each pair of lincRNAs and its PTGs obtained in the RNA-seq, respectively, while the r and p represent the mean in the 11 samples in quantitative verification. (a) MSTRG32975 vs. FUT4; (b) MSTRG306 vs. FEM1A; (c) MSTRG.7054 vs. GCGR; (d) MSTRG.29576 vs. DPYD.